Patoz

Protein Data Bank (pdb) file parser

⚠️ WIP This is a work in progress. Expect breaking changes frequently. Right now use at your own risk

📦 Cargo.toml

patoz = "0.1.0"

🔧 Examples

use std::{
    fs::File,
    io::{BufReader, Read},
    path::PathBuf,
};

use patoz::parse;

fn main() {
    let mut current_file_path = PathBuf::from(file!());
    current_file_path.pop();
    current_file_path.pop();
    current_file_path.push("1BYI.pdb");
    let content = read_file(&current_file_path);
    if let Ok((_, mut res)) = parse(&content) {
        println!(
            "Classification : {:?}",
            res.header().header().unwrap().classification
        );
        println!("Id Code : {:?}", res.header().header().unwrap().id_code);
        println!("Keywords : {:?}", res.header().keywds().unwrap().keywords);
    }
}

fn read_file(path: &PathBuf) -> String {
    let file = File::open(path).unwrap();
    let mut buf_reader = BufReader::new(file);
    let mut contents = String::new();
    if let Ok(_read_res) = buf_reader.read_to_string(&mut contents) {
        contents
    } else {
        "".to_owned()
    }
}

📊 Status

Record Parser Status

Title Section

• Header
• Obslte
• Title
• Splt
• Caveat
• Compnd
• Source
• Keywds
• Expdta
• Nummdl
• Mdltyp
• Author
• Sprsde
• Revdat
• Jrnl
  • Auth
  • Titl
  • Edit
  • Ref
  • Publ
  • Refn
  • Pmid
  • Doi
• Remarks

Primary Structure Section

• Dbref
• Dbref1
• Seqadv
• Seqres
• Modres

Heterogen Section

• Het
• Formul
• Hetnam
• Hetsyn

Secondary Structure Section

• Helix
• Sheet

Connectivity Annotation Section

• Ssbond
• Link
• Cispep

Miscellaneous Features Section

• Site

Crystallographic and Coordinate Transformation Section

• Cryst1
• MtrixN
• OrigxN
• ScaleN

Coordinate Section

• Model
• Atom
• Anisou
• Ter
• Hetatm
• Endmdl

Connectivity Section

• Conect

Bookkeeping Section

• Master
• End

📝 License

Licensed under MIT License (LICENSE).

🚧 Contributions

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the MIT license, shall be licensed as above, without any additional terms or conditions.